getYeastData           package:AnnBuilder           R Documentation

_F_u_n_c_t_i_o_n_s _t_o _g_e_t/_p_r_o_c_e_s_s _y_e_a_s_t _g_e_n_o_m_e _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     These functions extract data from the yeast genome web site based
     on a set of arguments.

_U_s_a_g_e:

     getYeastData(url, extenName, cols2Keep, sep)
     readBadData(url, sep)
     findNumCol(fewLines, sep)

_A_r_g_u_m_e_n_t_s:

     url: 'url' a character string for the url where yeast data are
          stored

extenName: 'extenName' a character string for the name of the data file
          of interest. The name can be a file name or with subdirectory
          names under "url"

cols2Keep: 'cols2Keep' a vector of index for the columns to be
          extracted from the data file

     sep: 'sep' a character string for the separater used to separate
          data columns in the data file

fewLines: 'fewLines' a set of character strings separated by a new line
          that is going to be used to determine how many data columns
          each line has

_D_e_t_a_i_l_s:

     The yeast genome web site has files stored in or in subdirectories
     of <URL: ftp://genome-ftp.stanford.edu/pub/yeast/data_download/>
     that can be downloaded. 'getYeastData' extracts data from a given
     file. The functions are used by an object of 'YG-class' to extract
     data.

     Some of the data in the web site may not be well fomatted (e.g.
     with missing columns). 'readBadData' deals with these type of data
     files.

     'findNumCol' figures out how many data columns a file contains
     based on a few entries from that file.

_V_a_l_u_e:

     'getYeastData' returns a matrix containing data.

     'readBadData' returns a matrix.

     'findNumCol' returns an integer.

_N_o_t_e:

     The functions are part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

_A_u_t_h_o_r(_s):

     Jianhua Zhang

_R_e_f_e_r_e_n_c_e_s:

     <URL: ftp://genome-ftp.stanford.edu/pub/yeast/data_download/>

_S_e_e _A_l_s_o:

     'YG-class'

_E_x_a_m_p_l_e_s:

     ## Not run: 
     # Url may change but was correct at the time of coding
     url <- "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/"
     temp <- getYeastData(url, "chromosomal_feature/SGD_features.tab",
                              cols2Keep = c(6, 1), sep = "\t")
     ## End(Not run)

